TB-Profiler result

Run: ERR2516071
Summary

Run ID: ERR2516071

Sample name:

Date: 31-03-2023 21:16:20

Number of reads: 409189

Percentage reads mapped: 99.7

Strain: lineage4.8

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
pncA 2288769 c.472delG frameshift_variant 0.12 pyrazinamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 6808 c.-494C>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491515 p.Asn245His missense_variant 0.15
mshA 576154 c.807C>T synonymous_variant 0.12
ccsA 620732 p.Ala281Val missense_variant 0.17
rpoB 762189 p.Ile795Val missense_variant 0.13
rpoC 764922 p.Glu518Gly missense_variant 0.11
rpoC 765452 p.Ala695Thr missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776086 p.Val799Ile missense_variant 0.12
mmpL5 776175 p.Ser769Phe missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406386 p.Ala319Ser missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476096 n.2439T>G non_coding_transcript_exon_variant 0.11
rpsA 1833400 c.-141delC upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101712 p.Gln444Leu missense_variant 0.11
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169149 c.1464G>C synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.25
PPE35 2170662 c.-50G>A upstream_gene_variant 0.18
Rv1979c 2222470 p.Phe232Ser missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714698 p.Arg212His missense_variant 0.12
folC 2746547 p.Asp351Gly missense_variant 0.13
pepQ 2859310 p.Ala370Gly missense_variant 0.29
pepQ 2860295 p.Ala42Pro missense_variant 0.12
ribD 2987560 p.Ala241Asp missense_variant 0.14
Rv2752c 3064814 p.Ile460Leu missense_variant 0.17
Rv3236c 3612133 c.984C>T synonymous_variant 0.2
Rv3236c 3612910 p.Leu69Phe missense_variant 0.25
fbiB 3641016 c.-519C>T upstream_gene_variant 0.1
alr 3840828 c.592dupG frameshift_variant 0.11
alr 3841515 c.-95C>T upstream_gene_variant 0.15
alr 3841535 c.-115G>A upstream_gene_variant 0.13
clpC1 4039652 c.1053G>C synonymous_variant 0.1
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040241 p.Thr155Phe missense_variant 0.11
clpC1 4040249 p.Glu152Gly missense_variant 0.12
embC 4239993 c.133_135delATC conservative_inframe_deletion 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244332 p.Val367Glu missense_variant 0.22
embA 4245244 p.Ala671Asp missense_variant 0.12
embA 4246255 p.Leu1008Pro missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0